[Biopython-dev] MSAprobs test fails

[Zheng Ruan]

I see. I was just trying different alignment program. In this case, it might
not be good to test the single sequence by the error code.

Zheng


On Tue, Apr 22, 2014 at 5:48 PM, Peter Cock <p.j.a.cock at googlemail.com>wrote:

> Hi Zheng,
>
> Negative error codes (from Python subprocess) are really Unix signals,
> https://docs.python.org/2/library/subprocess.html
>
> i.e. Linux killed the job with signal 11, probably SIGSEGV - Invalid
> memory reference.
>
>
> Can you run the tool by hand? Does it seg fault or something like that?
>
> Peter
>
> On Tue, Apr 22, 2014 at 10:18 PM, Zheng Ruan <zruan1991 at gmail.com> wrote:
> > Hi,
> >
> > The MASprobs wrapper fails when I run the test using the latest code. The
> > problem seems to be the err.returncode is -11 rather than 139, at least
> in
> > my machine (Linux 3.12 x86_64) python2.7 and 3.3 will both generate the
> > error.
> >
> > Here is scratch of the err message:
> >
> > FAIL: test_single_sequence
> (test_MSAProbs_tool.MSAProbsTestErrorConditions)
> > Test an input file containing a single sequence.
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "./test_MSAProbs_tool.py", line 86, in test_single_sequence
> >     stdout, stderr = cline()
> > Bio.Application.ApplicationError: Command 'msaprobs Fasta/f001' returned
> > non-zero exit status -11, '-------------------------------------'
> >
> > During handling of the above exception, another exception occurred:
> >
> > Traceback (most recent call last):
> >   File "./test_MSAProbs_tool.py", line 88, in test_single_sequence
> >     self.assertEqual(err.returncode, 139)
> > AssertionError: -11 != 139
> >
> >
> > Best,
> > Zheng Ruan
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>